Maher began the segment by first thanking Obama for giving atheists “a shout-out” at his first inaugural address, and at other times as president.

Maher then asked Obama about the lack of open and out atheists serving in public office. Obama responded by first expressing doubt about “whether there is active persecution of atheists.” However, Obama did go on to agree that atheists seeking political office faced a unique challenge:

I think you’re right, that there are certain occupations — probably, most prominently, politics — where there would be a bias against somebody who’s agnostic or atheist in running for office.

Later in the interview Obama lamented the problem with “fundamentalist extremism,” noting:

And where we get into problems, typically, is when our personal religious faith, or the community of faith that we participate in, tips into a sort of fundamentalist extremism, in which it’s not enough for us to believe what we believe, but we start feeling obligated to, you know, hit you over the head because you don’t believe the same thing. Or to treat you as somebody who’s less than I am.

In the interview Obama also stressed the importance of respect, at one point declaring:

… we should foster a culture in which people’s private religious beliefs, including atheists and agnostics, are respected.

Watch the entire segment on atheism below:

Transcript:

MAHER: I don’t know if anybody from my tribe of atheists ever thanked you for giving us a shout-out at your first inaugural…

OBAMA: I did.

MAHER: … but you did mention non-believers.

OBAMA: That’s right.

MAHER: I think–

OBAMA: More than once!

MAHER: More than once.

OBAMA: I mean, it’s not just in that speech. I’ve done it often.

MAHER: Well, we appreciate it. Because we do feel like untouchables to a degree. I mean, I don’t know if you saw the latest religion survey, but almost a quarter of the country are Nones. I don’t mean the ones who hit me on the knuckles with a ruler in Sunday School — I mean they put “None” for religion.

OBAMA: None of the above.

MAHER: Right… they’re atheists, agnostics, or they just don’t want to get up on Sunday morning. And we have no representation in Congress. If our numbers were represented, there’d be over a hundred congresspeople who felt that way. It just seems like we are not included in the basket of diversity in America, which is odd because we are the biggest minority. That is a bigger minority than any other minority you can name. Don’t you think we should get a little more love?

OBAMA: You know, I guess — my question would be whether there is active persecution of atheists. I think that there is certain… well, I think for a candidate… I think you’re right, that there are certain occupations — probably, most prominently, politics — where there would be a bias against somebody who’s agnostic or atheist in running for office. I think that’s still true. Outside of that arena, though? You seem to have done alright with your TV show… I mean, I don’t get a sense… to the extent that they’re boycotting you, it’s because of your other wacky views rather than your particular views on religion…

MAHER: [Laughs] What are my other wacky ideas? I usually agree with you!

OBAMA: I think the average American, if they go to the workplace, somebody’s next to ’em, they’re not poking around trying to figure out what their religious beliefs are. So here’s what I would say, that… we should foster a culture in which people’s private religious beliefs, including atheists and agnostics, are respected. And that’s the kind of culture that I think allows all of us, then, to believe what we want. That’s freedom of conscience. That’s what our Constitution guarantees. And where we get into problems, typically, is when our personal religious faith, or the community of faith that we participate in, tips into a sort of fundamentalist extremism, in which it’s not enough for us to believe what we believe, but we start feeling obligated to, you know, hit you over the head because you don’t believe the same thing. Or to treat you as somebody who’s less than I am.

MAHER: But we might be more pro-science in America if we were less religious, don’t you think?

OBAMA: Well… you know, I think that the issues we have with science these days are not restricted to what’s happening with respect to religion. There are a lot of very religious scientists around…

MAHER: Really?

OBAMA: … I think the problem here is that in our school systems, and to some degree — and this is where it is relevant — with school boards around the country that are mandating curriculums and textbooks, you start seeing this weird watering down of scientific fact so that our kids are growing up in an environment — and this connects to what I was saying earlier abou the media — where everything’s contested. Where nothing is true. Because if it’s on Facebook, it all looks the same. And if you’re reading something from a Nobel Prize-winning physicist next to some guy in his underwear writing in his basement, or his mom’s basement, on text, it looks like it’s equally plausible. And part of what we have to do a better job of, if our democracy is to function in a complicated diverse society like this, is to teach our kids enough critical thinking to be able to sort out what is true and what is false, what is contestable and what is incontestable. And we seem to have trouble with that. And our political system doesn’t help.